Background and Aim: Antioxidants are compounds that protect cells from attacks of free radicals. Lack of balance between antioxidants and free radicals results in oxidative stress, which ultimately results in cell damage. The effects of flavonoids are not related solely to their antioxidant properties, but also to their effects on cellular signal pathways. The present study was conducted to evaluate the effect of Quercetin on the structure of the third region of FGFR2b kinase using fluorescence method.Materials and Methods: Using SDS-PAGE, expression of the protein was determined and its constant concentration was used in the present study. Using different concentrations of Quercetin in the presence of a constant concentration of pure protein, the fluorescence spectrum and chemical denaturation were evaluated.Results: In the last studies, SDS-PAGE analysis of the purified proteins had confirmed that no contamination and unwanted bacterial proteins were co-eluted with the protein. Studying the spectrum of various concentrations of Quercetin in the presence of constant concentration of proteins showed a decrease in the intensity of the release; and also, the chemical denaturation changed the third structure of the kinase domain.Conclusion: The tertiary structural change of FGFR2b kinase domain represents a conformational change that may have a critical role in signal transduction cascade. Thus, this molecular transduction inconsistency can lead to cellular transduction complication; and as a result, inhibit the development and multiplication of cancerous cells.